The Government has been accused of "ecocide" over changes to the Emissions Trading Scheme that passed in Parliament last night.

The Climate Change Response (Emissions Trading and Other Matters) Amendment passed its third reading with support from the National Party and government partners.

But Green Party MP Kennedy Graham said the law change rips the heart out of the scheme. Taxpayers would now pick up the bill for polluters' carbon emissions, he said.

The law change delays the introduction of some industries into the regime and gives agriculture an indefinite reprieve from entry.

It passed 61-58, Labour, the Greens Party, NZ First, Mana and the Maori Party voted against it.

Graham said the Government had squandered the change to ensure New Zealand did its fair share on climate change.

"I charge them with the moral crime of ecocide." The scheme was already weak, now it was pointless, he said.

"The costs of pollution are loaded onto the shoulders of taxpayers and the National Government is doing nothing to incentivise clean technologies."

Climate Change Issues Minister Tim Groser said the amendments helped strike the right balance between doing our fair share and not impacting unreasonably on New Zealanders.

"Given the global economic climate, the Government needed to make tough decisions to not artificially inflate the short term cost of the ETS to households and businesses."

The changes would improve the administration and operation of the scheme while supporting economic growth, he said.

"These amendments will assist New Zealand in meeting its current and future international climate change obligations, ensure this is achieved at least cost to the domestic economy and provide the flexibility necessary to accommodate developments between now and 2015."